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PubMed2006

Commensurate (C6H14N2)2[Mo8O26] * 4H2O and incommensurate (C6H14N2)2[Mo8O26] * 4.66H2O: a structural versatility linked to solvent content.

The syntheses and structure determinations by means of single-crystal X-ray diffraction of commensurate (C(6)H(14)N(2))(2)[Mo(8)O(26)] * 4H(2)O and incommensurate (C(6)H(14)N(2))(2)[Mo(8)O(26)] * 4.66H(2)O, two new organic-inorganic hybrid compounds based on polyoxomolybdates and differing in their solvent content, are reported. Given the important disorder observed in the latter compound, only a combination of non-harmonic waves, crenel functions and TLS tensors offered a good modelling of the structure. (C(6)H(14)N(2))(2)[Mo(8)O(26)] * nH(2)O results from the self-assembly of [Mo(8)O(26)](4-) anionic chains, C(6)H(14)N(2)(2+) (H(2)DABCO(2+)) cations and water molecules. The [Mo(8)O(26)](4-) chain is built from gamma-[Mo(8)O(28)](8-) octamolybdate clusters, connected to each other through corner sharing. In both compounds, the [Mo(8)O(26)](4-) chains are separated, in a similar way, by the H(2)DABCO(2+) subunits, acting as charge-compensating cations, and by the water molecules. The orientation of the H(2)DABCO(2+) cations is shown to be different from what has been observed previously in monoclinic (H(2)DABCO)(2)[Mo(8)O(26)] * 4H(2)O, and therefore to give a different network of hydrogen bonds.

Crystallography, X-Ray↗

PubMed2002

Anisotropic behaviour of the C-terminal Kunitz-type domain of the alpha3 chain of human type VI collagen at atomic resolution (0.9 A).

The C-terminal Kunitz-type domain from the alpha3 chain of human type VI collagen (C5), a single amino-acid residue chain with three disulfide bridges, was refined at 0.9 A resolution in a monoclinic form, space group P2(1) with one molecule per asymmetric unit, using data collected at cryogenic temperature (110 K). The average protein factor decreases from 21 A(2) at room temperature (RT) to 12 A(2) at cryotemperature (100 K, CT). The spatially close N- and C-termini remain highly disordered. The different structural motifs of C5 were analyzed in terms of rigid-body displacement (TLS analyses) and show dominant libration motion for the secondary structure.

Amino Acid Motifs↗

PubMed2002

Refinement of the arginine kinase transition-state analogue complex at 1.2 A resolution: mechanistic insights.

The three-dimensional crystal structure of an arginine kinase transition-state analogue complex has been refined at 1.2 A resolution, with an overall R factor of 12.3%. The current model provides a unique opportunity to analyze the structure of a bimolecular (phosphagen kinase) enzyme in its transition state. This atomic resolution structure confirms in-line transfer of the phosphoryl group and the catalytic importance of the precise alignment of the substrates. The structure is consistent with a concerted proton transfer that has been proposed for an unrelated kinase. Refinement of anisotropic temperature factors and translation-libration-screw (TLS) analyses led to the identification of four rigid groups and their prevalent modes of motion in the transition state. The relative magnitudes of the mobility of rigid groups are consistent with their proposed roles in catalysis.

Animals↗

PubMed2003

Structure of dimeric cytochrome c3 from Desulfovibrio gigas at 1.2 A resolution.

The structure of dimeric cytochrome c(3) from the sulfate-reducing bacterium Desulfovibrio gigas, diDg, obtained by ab initio methods was further refined to 1.2 A resolution, giving final reliability factors of R(free) = 14.8% and R = 12.4%. This cytochrome is a dimer of tetraheme cytochrome c(3) molecules covalently linked by two solvent-accessible disulfide bridges, a characteristic unique to members of the cytochrome c(3) superfamily. Anisotropic analysis using the semi-rigid TLS method shows different behaviour for analogous loops in each monomer arising from their different packing environments. A detailed sequence and structural comparison with all other known cytochrome c(3) domains in single- and multi-domain cytochromes c(3) shows the presence of structurally conserved regions in this family, despite the high variability of the amino-acid sequence. An internal water molecule is conserved in a common structural arrangement in all c(3) tetraheme domains, indicating a probable electron-transfer pathway between hemes I and II. Unique features of diDg are an internal methionine residue close to heme I and to one of the axial ligands of heme III, where all other structures of the cytochrome c(3) superfamily have a phenylalanine, and a rather unusual CXXXCH heme-binding motif only found so far in this cytochrome.

Amino Acid Sequence↗

PubMed2005

The structure of F420-dependent methylenetetrahydromethanopterin dehydrogenase: a crystallographic 'superstructure' of the selenomethionine-labelled protein crystal structure.

The diffraction pattern of native protein crystals of F(420)-dependent methylenetetrahydromethanopterin dehydrogenase from Methanopyrus kandleri shows weak additional reflections compared with the selenomethionine-labelled protein crystals, indicating a doubled c unit-cell parameter. These reflections indicate small reorientations of the hexameric structural units, breaking the translational symmetry. TLS refinement of the selenomethionine-labelled protein structure at 1.55 A resolution revealed an anisotropic rigid-body libration of the hexameric units. The anisotropy is consistent with the static reorientation in the native protein crystals. These results are discussed as related to the crystal packing. The relation between the two structures suggests an analogy to structural changes during certain kinds of phase transitions that have been well studied in inorganic structural chemistry.

Crystallography, X-Ray↗

PubMed2006

Structural phase transition of monoclinic crystals of hen egg-white lysozyme.

Two monoclinic crystals (space group P2(1)) of hen egg-white lysozyme, a type I crystal grown at room temperature in a D2O solution with pD 4.5 containing 2%(w/v) sodium nitrate and a type II crystal grown at 313 K in a 10%(w/v) sodium chloride solution with pH 7.6, were each transformed into another monoclinic crystal with the same space group by dehydration-induced phase transition. Changes in X-ray diffraction were recorded to monitor the progress of the crystal transformation, which started with the appearance of diffuse streaks. In both crystals, the intensity of h + l odd reflections gradually weakened and finally disappeared on completion of the transformation. X-ray diffraction in the intermediate state indicated the presence of lattices of both the native and transformed crystals. In the native type I crystal, two alternate conformations were observed in the main chain of the region Gly71-Asn74. One conformer bound a sodium ion which was replaced with a water molecule in the other conformer. In the transformed crystal, the sodium ion was removed and the main-chain conformation of this region was converted to that of the water-bound form. The transformed crystal diffracted to a higher resolution than the native crystal, while the peak width of the diffraction spots increased. Analysis of the thermal motion of protein molecules using the TLS model has shown that the enhancement of the diffraction power in the transformed crystal is mainly ascribable to the suppression of rigid-body motion owing to an increase in intermolecular contacts as a result of the loss of bulk solvent.

Animals↗

PubMed2006

Structure of an orthorhombic form of xylanase II from Trichoderma reesei and analysis of thermal displacement.

An orthorhombic crystal of xylanase II from Trichoderma reesei was grown in the presence of sodium iodide. Crystal structures at atomic resolution were determined at 100 and 293 K. Protein molecules were aligned along a crystallographic twofold screw axis, forming a helically extended polymer-like chain mediated by an iodide ion. The iodide ion connected main-chain peptide groups between two adjacent molecules by an N-H...I-...H-N hydrogen-bond bridge, thus contributing to regulation of the molecular arrangement and suppression of the rigid-body motion in the crystal with high diffraction quality. The structure at 293 K showed considerable thermal motion in the loop regions connecting the beta-strands that form the active-site cleft. TLS model analysis of the thermal motion and a comparison between this structure and that at 100 K suggest that the fluctuation of these loop regions is attributable to the hinge-like movement of the beta-strands.

Binding Sites↗

PubMed1996

Molecular rigid-body displacements in a tetragonal lysozyme crystal confirmed by X-ray diffuse scattering.

X-ray diffuse scattering from protein crystals is, at the moment, the only available experimental process to be directly sensitive to long-range correlations between protein-atom displacements. It is shown here that calculations based on independent rigid-body displacements of individual molecules yield a description in good agreement with the experimental diffuse-scattering pattern displayed by tetragonal crystals of hen egg-white lysozyme (HEWL) In particular, it appears that molecular rigid-body translations and rigid- body rotations appear roughly in the same proportion as the average atomic mean-square positional fluctuations. The crystallographic temperature-factor analysis by TLS (translation/libration/screw) refinement, performed by Sternberg, Grace & Phillips [Sternberg, Grace, & Phillips (1979). J. Mol. Biol. 130, 231-253], is then confirmed and completed by a quantitative estimation of the molecular rigid-body translation contributions. The major contribution of molecular rigid- body displacements to the average atomic mean-square positional fluctuations, contradicts a previous analysis of the tetragonal HEWL diffuse-scattering data by Clarage, Clarage, Phillips, Sweet & Caspar [Clarage, Clarage, Phillips, Sweet & Caspar (1992). Proteins Struct. Funct. Genet. 12, 145-157] which concluded that short-range correlations dominate. The origin of these opposite conclusions mostly lies in the different hypotheses made to model diffuse scattering, underlying the limits of the 'homogeneous disorder' model.

Journal Article↗

PubMed1998

Structural parameters for proteins derived from the atomic resolution (1.09 A) structure of a designed variant of the ColE1 ROP protein.

The crystal structure of a designed variant of the ColE1 repressor of primer (ROP) protein has been refined with SHELXL93 to a resolution of 1.09 A. The final model with 510 non-H protein atoms, 576 H atoms in calculated positions and 114 water molecules converged to a standard R factor of 10% using unrestrained blocked full-matrix refinement. For all non-H atoms six-parameter anisotropic thermal parameters have been refined. The majority of atomic vibrations have a preferred orientation which is approximately perpendicular to the bundle axis; analysis with the TLS method [Schomaker & Trueblood (1968). Acta Cryst. B24, 63-77] showed a relatively good agreement between the individual atomic displacements and a rigid-body motion of the protein. Disordered residues with multiple conformations form clusters on the surface of the protein; six C-terminal residues have been omitted from the refined model due to disorder. Part of the solvent structure forms pentagonal or hexagonal clusters which bridge neighbouring protein molecules. Some water molecules are also conserved in wild-type ROP. The unrestrained blocked full-matrix least-squares refinement yielded reliable estimates of the standard deviations of the refined parameters. Comparison of these parameters with the stereochemical restraints used in various protein refinement programs showed statistically significant differences. These restraints should be adapted to the refinement of macromolecules by taking into account parameters determined from atomic resolution protein structures.

Anisotropy↗

PubMed1995

Establishment and characterization of IRTA17 and IRTA21, two novel acute non-lymphocytic leukaemia cell lines with t(16;21) translocation.

The t(16;21)(p11;q22) translocation is an infrequent chromosomal abnormality, but seems specific to acute non-lymphocytic leukaemia (ANLL). We established two cell lines with t(16;21)(p11;q22) from the bone marrow of a patient with ANL in relapse. Their morphological, karyotypic, immunohistochemical and genetic features are examined. Although both cell lines show monocytoid features morphologically, they express only CD13 (My7) and CD34, and neither expressed monocytoid or lymphoid markers. Reverse transcription-polymerase chain reaction showed that both cell lines expressed a similar TLS-ERG chimaeric mRNA as a result of the t(16;21)(p11;q22) translocation. As far as we know, there is no report of a leukaemia cell line with t(16;21). These cell lines represent a useful tool for leukaemia research.

Adult↗

PubMed1992

Pharmacodynamics of the anticonvulsant effect of oxazepam in aging BN/BiRij rats.

1. The purpose of this investigation was to examine the influence of increasing age on the pharmacokinetics and the time course of the anticonvulsant response of oxazepam in BN/BiRij rats as an animal model of aging. 2. Oxazepam was administered intravenously in a dose of 12 mg kg-1 body weight and the anticonvulsant effect intensity was measured as elevation above baseline of a threshold for induction of localized seizure activity (TLS). Direct cortical stimulation with ramp shaped electrical pulse trains of increasing intensity was used to determine this threshold. 3. The pharmacological effect vs. time profile showed in young rats an anticonvulsant component followed by proconvulsant component which is suggestive for the occurrence of acute tolerance and/or withdrawal syndrome. With increasing age the proconvulsant component disappeared, resulting in a monophasic effect profile (anticonvulsant effect only) at the age of 35 months with significantly higher anticonvulsant effect intensity immediately following drug administration. No age-related changes in the pharmacokinetic parameters of oxazepam were observed. 4. In five animals of each age group, benzodiazepine receptor binding characteristics were determined in vitro with [3H]-flunitrazepam as a ligand. Both receptor density and affinity did not show age-related changes. Available literature data on post-receptor events do not indicate conclusive age-related changes. 5. It is concluded, that the observed change in the pharmacodynamics of anticonvulsant effect of oxazepam can be explained by the disappearance of the tolerance/withdrawal phenomenon. This is compatible with a decreased efficiency of homeostatic control mechanisms in the elderly.

Aging↗

PubMed2003

Major age-related changes of mouse hematopoietic stem/progenitor cells.

To study age-related changes of mouse bone marrow (BM) cells and hematopoietic stem cells (HSCs), we isolated rhodamine-123(low) (Rh(low)) Thy1.1(low) Lin(-)Sca-1(+) (TLS) HSCs from the BM of old mice and compared their functional characteristics to cells of the same phenotype isolated from young mice. We observed impaired recovery of B lymphocytes and decreased self-renewal in recipients of old Rh(low) cells compared to young Rh(low) cells. Blockade of Rh efflux using verapamil improved lymphoid reconstitution by enriched HSCs, and isolation of aged HSCs based on efflux of a fluorescent multi-drug resistance (MDR) substrate (Bodipy-verapamil) resulted in enrichment of HSC activity equivalent to that obtained with Rh. These observations suggest a complex relationship between MDR activity and HSC function during aging. To address whether the difference between young and aged donors was intrinsic to the HSC compartment or was due to a shift in HSC phenotype, we co-transplanted normal BM derived from young or old donors and followed repopulation simultaneously in the same recipient animals. In a parallel experiment, we co-transplanted HSCs purified from old donors with BM derived from young donors. In both experiments, transplants were given to both young and old recipients. The results show a clear defect in B-cell engraftment from either BM or HSCs of old donors, irrespective of the age of the recipient. In contrast, myeloid engraftment was predominantly derived from BM or HSCs derived from aged donors, again irrespective of recipient age. These data suggest a stem cell basis for B-cell immuno-senescence and the increased incidence of myelocytic leukemia in elderly people.

Age Factors↗

PubMed2005

Modulation of cellular response to cisplatin by a novel inhibitor of DNA polymerase beta.

DNA polymerase beta (Pol beta) is an error-prone enzyme whose up-regulation has been shown to be a genetic instability enhancer as well as a contributor to cisplatin resistance in tumor cells. In this work, we describe the isolation of new Pol beta inhibitors after high throughput screening of 8448 semipurified natural extracts. In vitro, the selected molecules affect specifically Pol beta-mediated DNA synthesis compared with replicative extracts from cell nuclei. One of them, masticadienonic acid (MA), is particularly attractive because it perturbs neither the activity of the purified replicative Pol delta nor that of nuclear HeLa cell extracts. With an IC50 value of 8 microM, MA is the most potent of the Pol beta inhibitors found so far. Docking simulation revealed that this molecule could substitute for single-strand DNA in the binding site of Pol beta by binding Lys35, Lys68, and Lys60, which are the main residues involved in the interaction Pol beta/single-strand DNA. Selected inhibitors also affect the Pol beta-mediated translesion synthesis (TLS) across cisplatin adducts; MA was still the most efficient. Therefore, masticadienonic acid sensitized the cisplatin-resistant 2008C13*5.25 human tumor cells. Our data suggest that molecules such as masticadienonic acid could be suitable in conjunction with cisplatin to enhance anticancer treatments.

Animals↗

PubMed2005

Repair of the tRNA-like CCA sequence in a multipartite positive-strand RNA virus.

The 3' portions of plus-strand brome mosaic virus (BMV) RNAs mimic cellular tRNAs. Nucleotide substitutions or deletions in the 3'CCA of the tRNA-like sequence (TLS) affect minus-strand initiation unless repaired. We observed that 2-nucleotide deletions involving the CCA 3' sequence in one or all BMV RNAs still allowed RNA accumulation in barley protoplasts at significant levels. Alterations of CCA to GGA in only BMV RNA3 also allowed RNA accumulation at wild-type levels. However, substitutions in all three BMV RNAs severely reduced RNA accumulation, demonstrating that substitutions have different repair requirements than do small deletions. Furthermore, wild-type BMV RNA1 was required for the repair and replication of RNAs with nucleotide substitutions. Results from sequencing of progeny viral RNA from mutant input RNAs demonstrated that RNA1 did not contribute its sequence to the mutant RNAs. Instead, the repaired ends were heterogeneous, with one-third having a restored CCA and others having sequences with the only commonality being the restoration of one cytidylate. The role of BMV RNA1 in increased repair was examined.

Base Sequence↗

PubMed1996

Stress-induced binding of the transcriptional factor CHOP to a novel DNA control element.

CHOP (GADD153) is a mammalian nuclear protein that dimerizes with members of the C/EBP family of transcriptional factors. Absent under normal conditions, CHOP is induced by the stress encountered during nutrient deprivation, the acute-phase response, and treatment of cells with certain toxins. The basic region of CHOP deviates considerably in sequence from that of other C/EBP proteins, and CHOP-C/EBP heterodimers are incapable of binding to a common class of C/EBP sites. With respect to such sites, CHOP serves as an inhibitor of the activity of C/EBP proteins. However, recent studies indicate that certain functions of CHOP, such as the induction of growth arrest by overexpression of the wild-type protein and oncogenic transformation by the TLS-CHOP fusion protein, require an intact basic region, suggesting that DNA binding by CHOP may be implicated in these activities. In this study an in vitro PCR-based selection assay was used to identify sequences bound by CHOP-C/EBP dimers. These sequences were found to contain a unique core element PuPuPuTGCAAT(A/C)CCC. Competition in DNA-binding assays, DNase 1 footprint analysis, and methylation interference demonstrate that the binding is sequence specific. Deletions in the basic region of CHOP lead to a loss of DNA binding, suggesting that CHOP participates in this process. Stress induction in NIH 3T3 cells leads to the appearance of CHOP-containing DNA-binding activity. CHOP is found to contain a transcriptional activation domain which is inducible by cellular stress, lending further support to the notion that the protein can function as a positively acting transcription factor. We conclude that CHOP may serve a dual role both as an inhibitor of the ability of C/EBP proteins to activate some target genes and as a direct activator of others.

3T3 Cells↗

PubMed2005

Expression of a human cytochrome p450 in yeast permits analysis of pathways for response to and repair of aflatoxin-induced DNA damage.

Aflatoxin B1 (AFB1) is a human hepatotoxin and hepatocarcinogen produced by the mold Aspergillus flavus. In humans, AFB1 is primarily bioactivated by cytochrome P450 1A2 (CYP1A2) and 3A4 to a genotoxic epoxide that forms N7-guanine DNA adducts. A series of yeast haploid mutants defective in DNA repair and cell cycle checkpoints were transformed with human CYP1A2 to investigate how these DNA adducts are repaired. Cell survival and mutagenesis following aflatoxin B1 treatment was assayed in strains defective in nucleotide excision repair (NER) (rad14), postreplication repair (PRR) (rad6, rad18, mms2, and rad5), homologous recombinational repair (HRR) (rad51 and rad54), base excision repair (BER) (apn1 apn2), nonhomologous end-joining (NHEJ) (yku70), mismatch repair (MMR) (pms1), translesion synthesis (TLS) (rev3), and checkpoints (mec1-1, mec1-1 rad53, rad9, and rad17). Together our data suggest the involvement of homologous recombination and nucleotide excision repair, postreplication repair, and checkpoints in the repair and/or tolerance of AFB1-induced DNA damage in the yeast model. Rev3 appears to mediate AFB1-induced mutagenesis when error-free pathways are compromised. The results further suggest unique roles for Rad5 and abasic endonuclease-dependent DNA intermediates in regulating AFB1-induced mutagenicity.

Aflatoxin B1↗

PubMed1997

Differential patterns of osteoblast dysfunction in trabecular bone in patients with established osteoporosis.

AIMS: To analyse osteoblast function in 153 cases of established osteoporosis as previous work has indicated that osteoporosis is a heterogeneous condition characterised by different patterns of osteoclast and osteoblast dysfunction. METHODS: Histomorphometric data from 153 cases with established osteoporosis was used to analyse osteoblast function, using the following parameters: osteoblast number was assessed using the ratio of osteoblast surface to bone surface (ObS:BS); the percentage of active osteoblasts was assessed by using mineralising surface as a proportion of osteoid surface (sLS + dLS/OS); and the efficiency of active osteoblasts was assessed using the ratio of double to total labelled surface (dLS:tLS). The values of each parameter were standardised using age and sex matched control data and a three dimensional matrix was used to identify groups of patients with similar patterns of altered function. RESULTS: The largest group (60 cases) showed a reduction in all three parameters, while a small group (9 cases) had normal osteoblast function. However, one group showed reduction in osteoblast number only (23 cases), while another group showed a normal number of osteoblasts but both reduced percentage and efficiency of activity (14 cases). The results also suggest that efficiency of activity falls first and that this eventually leads to exit from the active pool. CONCLUSIONS: These results demonstrate the presence of heterogeneity of osteoblast dysfunction in osteoporosis, indicating that the disease is caused by interference at a variety of target sites along the pathway of osteoblast proliferation, differentiation, and activation. Greater understanding of this pathway and of the variety of alterations in the pathway that can occur in osteoporosis may allow more focused therapy for different patient groups identified on the basis of histomorphometric analysis.

Cell Count↗

PubMed2001

Malignant mesenchymoma of the lower leg.

A 24 year old man had a two year history of a painless mass on his right popliteal region. Magnetic resonance imaging demonstrated a 6 x 8 cm tumour mass in the lateral gastrocnemius. Histological examination of the tumour resected by radical surgery revealed that it consisted of myoblastic sarcoma and chondrosarcoma. Immunohistochemical studies were positive for Ki-67 and p53 throughout the area and for S-100 protein in the chondrosarcomatous area; in addition, they showed partial positivity for muscle common actin (HHF-35), smooth muscle actin, and myoglobin in the spindle cells. The percentages of Ki-67, p53, and p21/WAF1 positive cells in the spindle cell component were 34%, 65.7%, and < 0.1%, respectively. In addition, staining was negative for pancytokeratin, desmin, and glial fibrillary acidic protein. The SYT-SSX, TLS-CHOP, and EWS-FLI1 fusion genes were not detected using the reverse transcription polymerase chain reaction. Given the results, the definitive histological diagnosis is malignant mesenchymoma. This is the first report of malignant mesenchymoma of the lower leg with immunohistochemical and molecular studies.

Adult↗